Assume I have RNASeq data and a list of chromosome loci. Can I use some tools to get an output like this:
chr 2032121 A:20 T:350 C:300 G:55 chr 12098311 A:190 T:0 C:20 G:760
I want to calculate in each loci, how many A/T/C/G in the RNASeq reads. I am using samtools mpileup -l FILE -f hg19.fa in1.bam. But seems that can only identify the base on the reference genome. Thanks for help.